I believe there is a clear and present need across all science fields to make workflows more efficient, improve data management, and make our results accessible and digestible to general audiences. The first step toward this is to embrace analysis-to-product workflows in programs like R, and the second step is to share! Please feel free to check out my GitHub for code, make additions/edits, or let me know if you have comments. That’s how we make the best available science!


Help provide model-based estimates of abundance, distribution, Provide model-based estimates of abundance, distribution or age composition from AFSC

Groundfish Assessment Program (GAP) bottom trawl survey data to stock assessment authors and other requesters on a similar timeline as their equivalent design-based estimates. Such estimates can be included within stock assessment models or related analyses and reports (such as stock assessment and fishery evaluation, or SAFE reports), and may be subject to review by the relevant North Pacific Fishery Management Council Plan Team and Scientific and Statistical Committee (SSC).nd age composition from AFSC Groundfish Assessment Program (GAP) bottom trawl survey data to stock assessment authors and other requesters on a similar timeline as their equivalent design-based estimates. Such estimates can be included within stock assessment models or related analyses and reports (such as stock assessment and fishery evaluation, or SAFE reports), and may be subject to review by the relevant North Pacific Fishery Management Council Plan Team and Scientific and Statistical Committee (SSC).


GAP Survey Temperature Maps.

  • These scripts create the daily tempertaure and anomaly plots as NOAA Fisheries’ Alaska Fisheries Science Center conducts fisheries independant surveys in Alaska. The script pull temperature content from google drive and then push the maps to google drive for the communictions team.
  • Links: GitHub of R Package, Website where graphics are used!



R Markdown Reports


Alaska Fisheries Science Center Survey Data Reports.

  • Reproducibly automate groundfish data reports for all surveys conducted by the AFSC in R Markdown.
  • Links: GitHub of Repository


2021 Northern Bering Sea Groundfish and Crab Trawl Survey Highlights.

  • Reproducibly automate outreach reports for the Bering strait communities with results from the northern Bering sea survey conducted by the AFSC in R Markdown.
  • Links: GitHub of Private Repository


Fisheries Economics of the US Report.

  • Manage the redevelopment and production of the Fisheries Economics of the US report. This is a national-level report that provides ten years of economic information, impacts, and analyses related to U.S. commercial and recreational fishing activities and fishing-related industries. I am working to contemporize this iconic report by writing reproducible code using R and RMarkdown, which produces several report outputs and JavaScript files for the interactive FEUS online tool. All of this work has gone into improving this nationally regarded report for the many who reference it and making the process of producing it more streamlined, reproducible, and efficient.
  • Links: Website



R Packages


{NMFSReports}: Easily write NOAA reports and Tech Memos in R Markdown.

  • The NMFSReports Package has all of the basic architecture you need to create reproducible and repeatable NOAA Tech Memos in R Markdown! This approach is perfect for efficiently rolling out annual (or other regular) reports or reports with formulaic sections (the same chapter structure but for a different area or species). Scripts integrate table, figure, data, and bibliography management and design automation.
  • Links: Pkgdown Site for R Package


{FishEconProdOutput}: Measuring Output for U.S. Commercial Fisheries From Theory to Practice.

  • This package provides guidelines on fishery productivity measurement at the individual fishery and aggregate sector levels. Attention is given to the constructions of output and total factor productivity based on available data and a bottom-up approach. Given that there is no nation-wide standard cost survey, we recommend starting with measuring TFP at the fishery level based on a translog gross output production possibility frontier using index number techniques. Special attention is given to measuring quality-adjusted physical capital inputs in the bottom-up approach.
  • Links: Pkgdown Site for R Package


{GAPsurvey}: At-sea data management tools for RACE GAP surveys.

  • Catch, Length, and Specimen Data Import Program Instructions for at sea survey data for AFSC’s Gulf of Alaska and Bering Sea groundfish surveys.
  • Links: Pkgdown Site for R Package



R Shiny Applications


NOAA Fisheries Commerical, Recreational, and Aquaculture Fisheries Economic Impact R Shiny Model.

  • I/O models are used to assess economic activity such as jobs, income, and sales generated by a given industry sector. This is currently used in industry statistics (such as in FEUS) and management applications (to determine how a change would effect the economy, such as in planning team meetings).
  • Links: GitHub to R Package, GitHub to RShiny App


NOAA Fisheries Marine Mammal Acoustic Thresholds.

  • NMFS has provided this Web Calculator as an optional tool to provide estimated effect distances (i.e., isopleths) where PTS onset thresholds may be exceeded. Results provided by this calculator do not represent the entirety of the comprehensive effects analysis, but rather serve as one tool to help evaluate the effects of a proposed action on marine mammal hearing and make findings required by NOAA’s various statutes. Input values are the responsibility of the individual user.
  • Links: GitHub Repository, Shiny App



Research


Model-Based Abundance and Distribution Estimates using VAST.

  • Help provide model-based estimates of abundance, distribution, or age composition from AFSC Groundfish Assessment Program (GAP) bottom trawl survey data to stock assessment authors.
  • Links: GitHub of Private Repository, ModSquad


Modeling Environmentally Driven Distribution Shifts for Two Demersal, Migratory Species.

  • Habitat suitability models (HSMs) of summer flounder (Paralichthys dentatus) and black sea bass (Centropristis striata) were created using the fishery-independent Northeast Fisheries Science Center (NEFSC) bottom trawl survey data in generalized additive models and cumulative distribution functions. These analyses were used to probabilistically link where different length classes of these fish would likely be across different environmental variables in spring and fall. These different environmental variables (surface and bottom temperature and salinity, depth, and bottom type) have similar influences on life history of these two demersal, migratory, and commercially important species. Then, the HSMs were used to illustrate how the population’s distribution changed over time by hindcasting over regional ocean modeling systems (ROMS). The ROMS used in this analysis was a 1 Day Averaged ROMS for the Northeast US Coastline from 1958-2020.
  • Links: https://github.com/orgs/afsc-gap-products/teams/modsquad


 

© Copyright 2021 Emily Markowitz